If you're doing manual tool changes, unless your knee is CNC'd, don't even bother setting up the tool table - just change the tool, and zero it to the work using the knee, then hit CycleStart. If your knee is CNC'd, I have a set of macros that I wrote to use the knee for doing tool-length compensation, though this requires using custom macros in your G-code (M843 instead of G43, and M849 instead of G49) for turning tool length compensation on and off, due to limitations in Mach3 (That will be fixed in v4). I have another set of macros I use for setting up the tool table, using probing.
Regards,
Ray L.